YNDE - BACSU - GREMLIN Contacts

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YNDE - Spore germination protein YndE

UniProt:	O31809	Sequences: MFSPTSKITTAQATIIIINYMLAAGVLTLPRTVTEQTQSPDGWISVLLGGVLAVIAGMIIAKLSQQYPKETFYEYSRHIVGKWLGHLISIVFITYFLALGAFEVRVMSEIVDFFLLEGTPSWAIIMTVLWIGLYSITQGLDPIARLFEMIFPITVIIFLTIALMSLGIFEINNLRPVLGDGIMPVLRGVKTTNLSFTCSEIMFILVAFMKKPKNAVKAVVIGTGVVTSFYMITMIMVIGALSVEGVVTRTWPGLDLMRSFEIPGLIFERFESFLLVIWIMQLFATFIITFYAASLGVSQVFKKKPLSCMFGLLPVIYILSCMPKNENDVFILGDTVSHIALYIFGALPILLLVISKWRKRGEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	363 (346)
Sequences:	22615 (13989)
Seq/√Len:	752.0

ECOLI - POTE YJEH AROP GABP YIFK PHEP ARCD FRLA PROY LYSP YBAT ANSP ADIC CYCA MMUP CADB YJEM PLAP YCAM PUUP GADC YGJI TNAB MTR TYRP
BACSU - YNDE GERBB YBEC YTNA GERAB GERKB YBXG YHDG YECA ROCC YDGF ASPP YBGF ARCD YCGH AAPA HUTM YVBW STET GABP YFNA ROCE YFKT YDAO
HALSA - Q9HHU7 Q9HQB3 Q9HSL5
SULSO - Q97U05 Q97Y76 Q7LXI7 Q97XM0 Q97WS3 Q97ZB5 Q97X49 Q97YN3 Q97U33 Q97WD4 Q97VA6 Q97Z63 Q97VR4 Q97YX9 Q97VA8 Q97U39

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
133_L	317_Y	4.694	1.00
50_G	227_T	3.840	1.00
213_K	217_K	3.266	1.00
209_M	214_N	2.959	1.00
9_T	210_K	2.860	1.00
165_S	236_M	2.735	1.00
14_T	221_I	2.712	1.00
89_S	300_V	2.642	1.00
10_T	221_I	2.637	1.00
73_Y	303_K	2.626	1.00
208_F	295_L	2.578	1.00
269_R	273_F	2.429	1.00
298_S	302_K	2.418	1.00
13_A	209_M	2.367	1.00
207_A	302_K	2.359	1.00
314_P	318_I	2.314	1.00
10_T	14_T	2.301	1.00
134_Y	138_Q	2.300	1.00
255_D	258_R	2.283	1.00
10_T	214_N	2.254	1.00
217_K	221_I	2.221	1.00
9_T	12_Q	2.219	1.00
245_G	259_S	2.213	1.00
77_R	85_G	2.210	1.00
117_E	120_P	2.195	1.00
137_T	310_F	2.190	1.00
141_D	145_R	2.169	1.00
77_R	82_K	2.099	1.00
76_S	88_I	2.061	1.00
133_L	313_L	2.050	1.00
152_P	156_I	2.033	1.00
93_I	316_I	2.025	1.00
242_S	245_G	1.981	1.00
51_V	55_I	1.950	1.00
33_V	42_G	1.946	1.00
255_D	259_S	1.941	1.00
220_V	224_G	1.925	1.00
14_T	225_V	1.919	1.00
12_Q	148_E	1.909	1.00
17_I	222_G	1.871	1.00
126_M	321_C	1.860	1.00
130_W	317_Y	1.847	1.00
306_L	310_F	1.838	1.00
211_K	214_N	1.818	1.00
45_S	188_G	1.799	1.00
104_V	286_F	1.788	1.00
170_E	173_N	1.775	1.00
169_F	239_G	1.772	1.00
129_L	320_S	1.768	1.00
137_T	314_P	1.750	1.00
8_I	12_Q	1.748	1.00
263_P	269_R	1.743	1.00
353_V	357_W	1.739	1.00
258_R	271_E	1.713	1.00
205_L	291_Y	1.699	1.00
249_R	255_D	1.692	1.00
49_G	192_T	1.678	1.00
136_I	287_I	1.656	1.00
107_M	128_V	1.656	1.00
138_Q	306_L	1.653	1.00
111_V	124_I	1.634	1.00
100_G	320_S	1.630	1.00
12_Q	144_A	1.618	1.00
119_T	123_A	1.601	1.00
156_I	160_T	1.592	1.00
57_G	223_T	1.589	1.00
120_P	123_A	1.581	1.00
104_V	129_L	1.581	1.00
81_G	84_L	1.578	1.00
224_G	228_S	1.577	1.00
212_P	216_V	1.571	1.00
258_R	263_P	1.569	1.00
157_I	277_I	1.558	1.00
70_E	207_A	1.557	1.00
5_T	307_S	1.554	1.00
321_C	325_N	1.549	1.00
311_G	315_V	1.534	1.00
344_F	347_L	1.534	1.00
293_A	316_I	1.533	1.00
297_V	312_L	1.530	1.00
62_K	65_Q	1.528	1.00
57_G	219_V	1.526	1.00
10_T	217_K	1.519	1.00
67_Y	78_H	1.515	1.00
126_M	130_W	1.506	1.00
321_C	324_K	1.502	1.00
162_A	232_I	1.464	1.00
272_S	276_V	1.459	1.00
211_K	217_K	1.455	1.00
214_N	217_K	1.451	1.00
324_K	328_D	1.436	1.00
132_G	286_F	1.427	1.00
181_G	184_P	1.422	1.00
58_M	220_V	1.418	1.00
166_L	236_M	1.411	1.00
129_L	317_Y	1.402	1.00
107_M	279_I	1.382	1.00
161_I	165_S	1.378	1.00
74_E	78_H	1.378	1.00
41_D	178_L	1.378	1.00
80_V	84_L	1.365	1.00
165_S	240_A	1.363	1.00
21_M	226_V	1.360	1.00
43_W	235_I	1.351	1.00
228_S	232_I	1.341	1.00
325_N	328_D	1.339	1.00
59_I	351_L	1.338	1.00
261_E	270_F	1.327	1.00
133_L	314_P	1.325	1.00
294_S	313_L	1.323	1.00
86_H	90_I	1.320	1.00
155_V	159_L	1.319	1.00
173_N	176_P	1.318	1.00
41_D	185_V	1.299	1.00
116_L	119_T	1.290	1.00
172_N	175_R	1.281	1.00
13_A	218_A	1.276	1.00
170_E	174_L	1.262	1.00
18_I	225_V	1.258	1.00
347_L	355_S	1.255	1.00
64_S	75_Y	1.251	1.00
60_I	72_F	1.249	1.00
7_K	210_K	1.246	1.00
69_K	74_E	1.242	1.00
251_W	255_D	1.239	1.00
146_L	150_I	1.233	1.00
28_T	106_V	1.233	1.00
167_G	172_N	1.231	1.00
8_I	13_A	1.230	1.00
352_L	356_K	1.227	1.00
122_W	126_M	1.207	1.00
93_I	297_V	1.206	1.00
351_L	355_S	1.204	1.00
103_E	285_T	1.203	1.00
11_A	15_I	1.203	1.00
16_I	205_L	1.203	1.00
133_L	137_T	1.202	1.00
8_I	144_A	1.199	1.00
210_K	214_N	1.188	1.00
177_V	180_D	1.169	1.00
17_I	202_M	1.167	1.00
171_I	174_L	1.160	1.00
34_T	42_G	1.156	1.00
311_G	314_P	1.155	1.00
150_I	284_A	1.149	1.00
169_F	173_N	1.148	1.00
108_S	124_I	1.147	1.00
167_G	171_I	1.129	1.00
80_V	356_K	1.125	1.00
160_T	164_M	1.118	1.00
73_Y	299_Q	1.115	1.00
169_F	174_L	1.114	1.00
235_I	239_G	1.112	1.00
249_R	252_P	1.107	1.00
47_L	231_M	1.097	1.00
145_R	149_M	1.097	1.00
83_W	87_L	1.090	1.00
18_I	226_V	1.090	1.00
132_G	287_I	1.084	1.00
69_K	78_H	1.083	1.00
347_L	353_V	1.079	1.00
131_I	283_F	1.077	1.00
102_F	194_L	1.073	1.00
80_V	352_L	1.065	1.00
167_G	170_E	1.065	1.00
147_F	287_I	1.062	1.00
170_E	176_P	1.058	1.00
242_S	259_S	1.055	1.00
135_S	146_L	1.050	1.00
127_T	131_I	1.050	1.00
171_I	175_R	1.043	1.00
137_T	308_C	1.043	1.00
43_W	238_I	1.039	1.00
10_T	218_A	1.038	1.00
76_S	84_L	1.038	1.00
130_W	134_Y	1.033	1.00
168_I	171_I	1.031	1.00
333_G	336_V	1.024	1.00
140_L	291_Y	1.021	1.00
206_V	215_A	1.019	1.00
124_I	127_T	1.008	1.00
200_E	204_I	1.007	1.00
15_I	148_E	1.001	1.00
111_V	279_I	0.989	1.00
162_A	166_L	0.985	1.00
350_L	353_V	0.981	1.00
108_S	125_I	0.974	1.00
107_M	283_F	0.971	1.00
324_K	327_N	0.970	1.00
240_A	256_L	0.969	1.00
134_Y	137_T	0.966	1.00
7_K	141_D	0.966	1.00
118_G	121_S	0.962	1.00
159_L	163_L	0.960	1.00
55_I	59_I	0.960	1.00
145_R	148_E	0.954	1.00
340_A	347_L	0.954	1.00
77_R	303_K	0.951	1.00
348_P	351_L	0.949	1.00
155_V	229_F	0.947	1.00
88_I	349_I	0.946	1.00
22_L	25_G	0.932	1.00
161_I	257_M	0.927	1.00
54_V	220_V	0.925	1.00
111_V	115_L	0.925	1.00
347_L	350_L	0.921	1.00
326_E	329_V	0.915	1.00
117_E	121_S	0.914	1.00
295_L	298_S	0.910	1.00
227_T	231_M	0.907	1.00
50_G	196_F	0.903	1.00
12_Q	145_R	0.903	1.00
322_M	326_E	0.902	1.00
305_P	310_F	0.898	1.00
123_A	127_T	0.898	1.00
54_V	58_M	0.895	1.00
92_F	96_F	0.895	1.00
221_I	225_V	0.892	1.00
323_P	328_D	0.892	1.00
172_N	176_P	0.889	1.00
40_P	238_I	0.885	1.00
107_M	282_L	0.884	1.00
257_M	262_I	0.880	1.00
138_Q	142_P	0.879	1.00
154_T	281_Q	0.879	1.00
322_M	325_N	0.878	1.00
14_T	218_A	0.877	1.00
80_V	353_V	0.875	1.00
310_F	314_P	0.873	1.00
62_K	66_Q	0.869	1.00
62_K	355_S	0.868	1.00
132_G	283_F	0.864	1.00
290_F	317_Y	0.862	1.00
168_I	172_N	0.862	1.00
162_A	236_M	0.861	1.00
21_M	222_G	0.860	1.00
125_I	324_K	0.856	1.00
187_R	191_T	0.855	1.00
11_A	145_R	0.851	1.00
169_F	172_N	0.849	1.00
178_L	185_V	0.845	1.00
44_I	185_V	0.844	1.00
211_K	216_V	0.838	1.00
116_L	120_P	0.836	1.00
132_G	290_F	0.835	1.00
350_L	355_S	0.834	1.00
63_L	75_Y	0.833	1.00
347_L	357_W	0.832	1.00
201_I	292_A	0.830	1.00
97_L	319_L	0.825	1.00
33_V	192_T	0.825	1.00
26_V	233_T	0.819	1.00
105_R	332_L	0.813	1.00
44_I	47_L	0.811	1.00
44_I	48_L	0.811	1.00
11_A	148_E	0.809	1.00
295_L	309_M	0.805	1.00
137_T	306_L	0.803	1.00
116_L	121_S	0.797	1.00
108_S	121_S	0.794	1.00
269_R	272_S	0.792	1.00
136_I	291_Y	0.790	1.00
118_G	122_W	0.783	1.00
42_G	234_M	0.782	1.00
19_N	151_F	0.779	1.00
130_W	321_C	0.778	1.00
354_I	357_W	0.777	1.00
182_I	186_L	0.777	1.00
309_M	312_L	0.777	1.00
59_I	348_P	0.775	1.00
323_P	326_E	0.775	1.00
332_L	336_V	0.772	1.00
7_K	140_L	0.771	1.00
346_A	350_L	0.771	1.00
207_A	298_S	0.770	1.00
168_I	173_N	0.770	1.00
232_I	236_M	0.770	1.00
83_W	86_H	0.769	1.00
169_F	176_P	0.768	1.00
209_M	215_A	0.768	1.00
262_I	270_F	0.766	1.00
171_I	239_G	0.763	1.00
182_I	185_V	0.760	1.00
332_L	355_S	0.756	1.00
174_L	238_I	0.752	1.00
349_I	353_V	0.750	1.00
340_A	343_I	0.750	1.00
197_T	343_I	0.748	1.00
225_V	229_F	0.746	1.00
323_P	327_N	0.743	1.00
73_Y	77_R	0.743	1.00
233_T	237_V	0.742	1.00
30_P	234_M	0.741	1.00
61_A	65_Q	0.741	1.00
290_F	294_S	0.736	1.00
203_F	219_V	0.735	1.00
170_E	175_R	0.732	1.00
112_D	121_S	0.732	1.00
171_I	176_P	0.727	1.00
142_P	145_R	0.727	1.00
166_L	232_I	0.726	1.00
162_A	233_T	0.725	1.00
144_A	148_E	0.725	1.00
110_I	278_W	0.724	1.00
113_F	275_L	0.722	1.00
281_Q	284_A	0.719	1.00
53_A	199_S	0.719	1.00
32_T	35_E	0.717	1.00
46_V	195_S	0.717	1.00
139_G	142_P	0.716	1.00
178_L	181_G	0.714	1.00
197_T	200_E	0.713	1.00
215_A	219_V	0.711	1.00
33_V	38_Q	0.710	1.00
330_F	334_D	0.710	1.00
22_L	154_T	0.709	1.00
169_F	175_R	0.708	1.00
43_W	47_L	0.707	1.00
7_K	11_A	0.707	1.00
23_A	27_L	0.705	1.00
257_M	261_E	0.704	1.00
47_L	51_V	0.704	1.00
20_Y	289_T	0.703	1.00
213_K	216_V	0.703	1.00
57_G	199_S	0.702	1.00
216_V	219_V	0.695	1.00
341_L	344_F	0.694	1.00
11_A	14_T	0.690	1.00
130_W	133_L	0.689	1.00
335_T	339_I	0.689	1.00
73_Y	89_S	0.689	1.00
128_V	286_F	0.689	1.00
144_A	287_I	0.688	1.00
126_M	325_N	0.682	1.00
22_L	27_L	0.679	1.00
46_V	234_M	0.679	1.00
208_F	309_M	0.678	1.00
20_Y	288_I	0.678	1.00
64_S	215_A	0.676	1.00
136_I	313_L	0.676	1.00
14_T	17_I	0.676	1.00
49_G	196_F	0.674	1.00
57_G	61_A	0.673	1.00
88_I	346_A	0.673	1.00
81_G	85_G	0.673	1.00
114_F	279_I	0.672	1.00
293_A	297_V	0.669	1.00
111_V	128_V	0.668	1.00
351_L	354_I	0.666	1.00
63_L	79_I	0.663	1.00
344_F	355_S	0.663	1.00
301_F	304_K	0.662	1.00
64_S	203_F	0.661	1.00
54_V	224_G	0.661	1.00
48_L	189_V	0.659	1.00
330_F	333_G	0.659	1.00
170_E	239_G	0.658	1.00
70_E	298_S	0.657	1.00
168_I	174_L	0.655	1.00
103_E	286_F	0.654	1.00
79_I	350_L	0.652	1.00
252_P	256_L	0.651	1.00
204_I	292_A	0.649	1.00
54_V	223_T	0.649	1.00
347_L	351_L	0.649	1.00
18_I	151_F	0.648	1.00
176_P	179_G	0.646	1.00
178_L	182_I	0.645	1.00
40_P	43_W	0.644	1.00
334_D	337_S	0.644	1.00
24_A	194_L	0.641	1.00
338_H	342_Y	0.640	1.00
41_D	177_V	0.639	1.00
257_M	270_F	0.638	1.00
117_E	122_W	0.637	1.00
315_V	319_L	0.636	1.00
340_A	350_L	0.636	1.00
96_F	289_T	0.634	1.00
148_E	152_P	0.633	1.00
286_F	289_T	0.632	1.00
43_W	231_M	0.630	1.00
257_M	260_F	0.628	1.00
297_V	315_V	0.626	1.00
71_T	203_F	0.624	1.00
73_Y	85_G	0.622	1.00
142_P	146_L	0.621	1.00
350_L	354_I	0.619	1.00
251_W	254_L	0.619	1.00
321_C	328_D	0.617	1.00
126_M	323_P	0.616	1.00
294_S	312_L	0.616	1.00
340_A	344_F	0.616	1.00
339_I	343_I	0.614	1.00
49_G	193_N	0.611	1.00
72_F	200_E	0.610	1.00
151_F	154_T	0.609	1.00
273_F	277_I	0.607	1.00
174_L	239_G	0.607	1.00
310_F	313_L	0.606	1.00
104_V	108_S	0.603	1.00
149_M	153_I	0.603	1.00
106_V	110_I	0.602	1.00
236_M	239_G	0.601	1.00
133_L	290_F	0.599	1.00
20_Y	201_I	0.599	1.00
114_F	276_V	0.598	1.00
23_A	230_Y	0.598	1.00
119_T	122_W	0.598	1.00
164_M	262_I	0.597	1.00
342_Y	347_L	0.594	1.00
331_I	334_D	0.593	1.00
140_L	205_L	0.593	1.00
314_P	317_Y	0.593	1.00
137_T	313_L	0.592	1.00
72_F	204_I	0.592	1.00
338_H	341_L	0.592	1.00
99_L	103_E	0.591	1.00
6_S	210_K	0.591	1.00
76_S	85_G	0.588	1.00
164_M	261_E	0.588	1.00
184_P	187_R	0.586	1.00
342_Y	357_W	0.584	1.00
325_N	329_V	0.582	1.00
103_E	282_L	0.582	1.00
17_I	21_M	0.580	1.00
41_D	44_I	0.580	1.00
30_P	237_V	0.580	1.00
348_P	355_S	0.577	1.00
107_M	111_V	0.577	1.00
224_G	227_T	0.577	1.00
22_L	229_F	0.575	1.00
237_V	253_G	0.575	1.00
143_I	291_Y	0.575	1.00
221_I	224_G	0.573	1.00
343_I	347_L	0.572	1.00
60_I	350_L	0.571	1.00
91_V	346_A	0.571	1.00
128_V	283_F	0.569	1.00
28_T	31_R	0.569	1.00
240_A	260_F	0.568	1.00
276_V	280_M	0.567	1.00
108_S	111_V	0.567	1.00
230_Y	234_M	0.566	1.00
324_K	329_V	0.566	1.00
131_I	135_S	0.564	1.00
99_L	102_F	0.564	1.00
76_S	353_V	0.563	1.00
344_F	348_P	0.563	1.00
225_V	228_S	0.561	1.00
110_I	254_L	0.560	1.00
114_F	275_L	0.559	1.00
87_L	91_V	0.559	1.00
233_T	253_G	0.557	1.00
118_G	123_A	0.557	1.00
27_L	158_F	0.554	1.00
101_A	104_V	0.553	1.00
56_A	200_E	0.553	1.00
204_I	296_G	0.552	1.00
63_L	66_Q	0.551	1.00
46_V	230_Y	0.551	1.00
290_F	316_I	0.550	1.00
328_D	331_I	0.549	1.00
297_V	301_F	0.548	1.00
241_L	245_G	0.547	1.00
103_E	106_V	0.545	1.00
128_V	132_G	0.545	1.00
337_S	344_F	0.544	1.00
352_L	355_S	0.543	1.00
45_S	185_V	0.542	1.00
50_G	54_V	0.541	1.00
156_I	159_L	0.541	1.00
15_I	151_F	0.541	1.00
130_W	314_P	0.540	1.00
97_L	316_I	0.539	1.00
263_P	272_S	0.539	1.00
348_P	352_L	0.539	1.00
329_V	333_G	0.538	1.00
147_F	288_I	0.536	1.00
339_I	347_L	0.535	1.00
9_T	214_N	0.532	1.00
125_I	322_M	0.531	1.00
58_M	62_K	0.531	1.00
344_F	351_L	0.530	1.00
8_I	140_L	0.526	1.00
252_P	257_M	0.526	1.00
159_L	229_F	0.523	1.00
272_S	275_L	0.522	1.00
173_N	239_G	0.519	1.00
103_E	194_L	0.519	1.00
7_K	307_S	0.518	1.00
56_A	348_P	0.517	1.00
353_V	356_K	0.516	1.00
344_F	357_W	0.515	1.00
153_I	157_I	0.515	1.00
202_M	219_V	0.515	1.00
241_L	255_D	0.514	1.00
209_M	218_A	0.512	1.00
13_A	205_L	0.512	1.00
153_I	277_I	0.512	1.00
91_V	95_Y	0.510	1.00
202_M	215_A	0.510	1.00
84_L	87_L	0.509	1.00
336_V	340_A	0.509	1.00
84_L	349_I	0.508	1.00
28_T	282_L	0.508	1.00
40_P	243_V	0.508	1.00
69_K	207_A	0.507	1.00
259_S	263_P	0.506	1.00
85_G	89_S	0.506	1.00
186_L	190_K	0.505	1.00
335_T	338_H	0.505	1.00
30_P	33_V	0.504	1.00
168_I	175_R	0.503	1.00
63_L	67_Y	0.502	1.00
26_V	158_F	0.502	1.00
263_P	271_E	0.502	1.00
61_A	219_V	0.501	1.00
61_A	216_V	0.501	1.00
13_A	202_M	0.500	1.00

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3l1lA	2	0.9504	100	0.259	Contact Map
3giaA	1	0.9697	100	0.297	Contact Map
4djkA	2	0.9394	100	0.358	Contact Map
3dh4A	3	0.9477	98.8	0.826	Contact Map
2xq2A	2	0.9477	98.8	0.827	Contact Map
2jlnA	1	0.9614	98.6	0.841	Contact Map
4wgvA	2	0.9174	98	0.863	Contact Map
4us3A	1	0.9669	97.7	0.873	Contact Map
2a65A	2	0.9669	97.5	0.879	Contact Map
4xp4A	1	0.9532	97.2	0.885	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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